Import pairwise contrasts from a file

importPairwiseContrasts(
  file,
  groupCol = "group",
  numeratorCol = "numerator",
  denominatorCol = "denominator",
  namesCol = "description"
)

Arguments

file

character(1). File path.

groupCol

character(1). Group column name in colData() of DESeqDataSet. Corresponds to value in design().

numeratorCol

character(1). Numerator column name in contrasts file.

denominatorCol

character(1). Denominator column name in contrasts file.

namesCol

character(1). Column in contrasts file to used to define the names of the contrast list. Values will be sanitized into snakeCase().

Value

list. Named list of pairwise character vectors containing: "group", "numerator", "denominator".

Note

Updated 2019-09-09.

See also

Examples

file <- system.file("extdata/contrasts.csv", package = "DESeqAnalysis") x <- importPairwiseContrasts(file)
#> → Importing contrasts.csv at /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp9QrS1N/temp_libpathf12f54c6159b/DESeqAnalysis/extdata using vroom::`vroom()`.
print(x)
#> $dox_induction_control #> group numerator denominator #> "group" "B" "A" #> #> $effect_of_wt_protein_induction_vs_ev_line #> group numerator denominator #> "group" "C" "B" #>